Actually, configuration files are a "mirror" of the database. Every time you open or modify your project it gets information from its configuration files. Right before that configuration files verify that same configurations are available in the database, and only when this condition is fulfilled, information is send to your project. In other words, when your config file is opened, it connects to the database, makes sure that configurations at both places are the identical and then sends information for a change (dummy change) to your project . That's why you get a "file has changed" massage when no actual change has been done. With the release of Sitefinity 4.0 you are able to move your configuration files to the database, as shown in this blog post
. If this is done, there won't be any verification between your project and the database and you won't get warning messages.
the Telerik team
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system and vote to affect the priority of the items